Today I tagged the beta for the 2012.06 (Q3 2012 in the old numbering) release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_06_1beta1/
and uploaded a source distribution to the google code site: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2012_06_1beta1.tgz If there's demand for it, I will also put up a windows binary. As usual: if no show-stopper bugs appear, I will do the release itself in about a week. This release has a relatively small number of new features, but a large number of bug fixes and some performance enhancements. Excerpts from the release notes are below. Best Regards, -greg ****** Release_2012.06.1 ******* (Changes relative to Release_2012.03.1) !!!!!! IMPORTANT !!!!!! - Some of the bug fixes affect the generation of SMILES. Canonical SMILES generated with this version of the RDKit will be different from previous versions. Acknowledgements: Andrew Dalke, JP Ebejer, Igor Filippov, Peter Gedeck, Jan Holst Jensen, Adrian Jasiński, George Papadatos, Andrey Paramonov, Adrian Schreyer, James Swetnam Bug Fixes: - Radicals are now indicated in molecular depictions. (Issue 3516995) - Calling .next() on an SDMolSupplier at eof no longer results in an infinite loop. (Issue 3524949) - Chirality perception no longer fails in large molecules. (Issue 3524984) - problem creating molblock for atom with four chiral nbrs (Issue 3525000) - A second sanitization leads to a different molecule. (Issue 3525076) - can't parse Rf atom in SMILES (Issue 3525668) - generates [HH2-] but can't parse it (Issue 3525669) - improper (re)perception of 1H-phosphole (Issue 3525671) - ForwardSDMolSupplier not skipping forward on some errors (Issue 3525673) - SMILES/SMARTS parsers don't recognize 0 atom maps (Issue 3525776) - R group handling in SMILES (Issue 3525799) - Canonical smiles failure in symmetric heterocycles (Issue 3526810) - Canonical smiles failure with "extreme" isotopes (Issue 3526814) - Canonical smiles failure with many symmetric fragments (Issue 3526815) - Canonical smiles failure with dependent double bonds (Issue 3526831) - Build Fails Due to Missing include in Code/RDBoost/Wrap.h (Issue 3527061) - Incorrect template parameter use in std::make_pair (Issue 3528136) - Canonicalization failure in cycle (Issue 3528556) - incorrect values reported in ML analysis (Issue 3528817) - Cartridge does not work on 32bit ubuntu 12.04 (Issue 3531232) - Murcko Decomposition generates unuseable molecule. (Issue 3537675) - A few memory leaks were fixed in the Java Wrappers - The exact mass of molecules with non-standard isotopes is now calculated correctly. - The default (Euclidean) distance metric should now work with Butina clustering. - Some bugs in the depictor were fixed. New Features: - ChemicalFeatures now support an optional id - Isotope handling has been greatly improved. Atoms now have a getIsotope() (GetIsotope() in Python) method that returns zero if no isotope has been set, the isotope number otherwise. - The function MolFragmentToSmiles can be used to generate canonical SMILES for pieces of molecules. - The function getHashedMorganFingerprint (GetHashedMorganFingerprint in Python) has been added. New Database Cartridge Features: New Java Wrapper Features: Deprecated modules (to be removed in next release): Removed modules: - rdkit.Excel - the code in $RDBASE/Code/PgSQL/RDLib Other: - Similarity calculations on ExplicitBitVectors should now be much faster - Use of [Xa], [Xb], etc. for dummy atoms in SMILES is no longer possible. Use the "*" notation and either isotopes (i.e. [1*], [2*]) or atom maps (i.e. [*:1], [*:2]) instead. - Initial work was done towards make the RDKit work on big endian hardware (mainly changes to the way pickles are handled) - Canonical SMILES generation is now substantially faster. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-devel mailing list Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
